Modular optical analytic systems and methods

ABSTRACT

A system includes a plurality of modular subassemblies and a plate; wherein each modular subassembly comprises an enclosure and a plurality of optical components aligned to the enclosure, and each enclosure comprises a plurality of mounting structures; and wherein each modular subassembly is mechanically coupled to the plate by attachment of a mounting structure of the modular subassembly directly to a corresponding mounting structure located on the plate, such that by mechanically coupling each modular subassembly to the plate using the mounting structure of the modular subassembly and the corresponding mounting structure on the plate, adjacent modular subassemblies are aligned to each other upon such attachment, and wherein two of the modular subassemblies mechanically coupled to the plate are also attached to each other by mechanically coupling an alignment structure on one of the two modular subassemblies to a respective alignment structure on the other of the two modular subassemblies.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 15/847,428 filed on Dec. 19, 2017, which claims the benefit ofU.S. Provisional Patent Application No. 62/442,937 filed on Jan. 5, 2017and GB Patent Application No. 1704771.3 filed on Mar. 24, 2017, all ofwhich are incorporated by reference herein in their entirety.

BACKGROUND

Biological optical analysis instruments, such as genetic sequencers,tend to include multiple configurable components, each with multipledegrees of freedom. Increasing complexity of these biological opticalanalysis instruments has led to increased manufacturing and operationexpense. Generally, these types of instruments benefit from precisealignment of their many internal optical components. In some geneticsequencing instruments, for example, internal components are generallyaligned within precise tolerances. Many manufacturing techniques forsuch instruments involve installing all of the components on a precisionplate, and then configuring and aligning each component. Componentalignment may change during shipping or use. For example, temperaturechanges may alter alignments. Re-aligning each component takes time andskill. In some examples, there may be over 30 total degrees of freedomavailable across all of the components and they interact to each other.The large number of degrees of freedom complicates alignment andconfiguration and adds time and expense to system operation. Opticalsequencer fabrication and operation may be simplified by reducing thedegrees of freedom available across all system components through amodular architecture.

SUMMARY

Various implementations of the technologies disclosed herein providemodular optical analytic systems. For example, a modular opticalanalytic system may be used to analyze biological samples, such as inthe case of a genetic sequencer. Other examples of the technologiesdisclosed herein provide methods for manufacturing, configuring, andoperating modular optical analytic systems.

In some examples, grouping components of a modular optical analyticsystem into modular sub-assemblies, and then installing the modularsub-assemblies on a precision plate or other stable structure may reducerelative degrees of freedom and simplify overall system maintenance. Forexample, in one example, a modular optical analytic system may includesets of components grouped into four modular subassemblies. A firstmodular subassembly may include a plurality of lasers and correspondinglaser optics grouped together into a line generation module (LGM). Asecond modular subassembly may include lenses, tuning and filteringoptics grouped into an emission optics module (EOM). A third modularsubassembly may include camera sensors and corresponding optomechanicsgrouped into a camera module (CAM). A fourth modular subassembly mayinclude focus tracking sensors and optics grouped into a focus trackingmodule (FTM). In some implementations, components of the system maygroup into different modular subassemblies. Components may be groupedinto fewer or greater numbers of subassemblies depending on the specificapplication and design choices. Each modular subassembly may bepre-fabricated by incorporating the individual components onto amounting plate or enclosure and precisely aligning and configuring thecomponents within the modular sub-assembly to predetermined tolerances.Each modular sub-assembly may be fabricated to minimize degrees offreedom, such that only key components may be moved in one or moredirections, or rotated, to enable precision alignment.

The system may also include a precision mounting plate. The precisionmounting plate may be fabricated with alignment surfaces, such asmounting pins, grooves, slots, grommets, tabs, magnets, datum surfaces,tooling balls, or other surfaces designed to accept and mount eachpre-fabricated and tested modular subassembly in its desired position.The precision mounting plate need may include flat structures, non-flatstructures, solid structures, hollow structures, honeycombed or latticedstructures, or other types of rigid mounting structures as known in theart. In some examples, the precision mounting plate incorporates or iscoupled to a stage motion assembly configured to maintain a levelmounting surface and dampen vibration. The stage assembly may includeactuators to control one or more control surfaces of an optical targetto provide feedback to align the modular subassemblies, for example, toreposition one or more optical components or sensors withinpredetermined tolerances. The stage assembly may also include one ormore sample holders, and may include precision motion devices toaccurately position the samples within or through the field of view ofthe optical imaging system, in stepwise or continuous motions.

Assembling a modular optical analytic system may include mounting eachmodular sub-assembly on the precision mounting plate and performing afinal alignment using one or more control adjustments. In someimplementations, an optical analytic system with more than 30 degrees offreedom across each of its components may be reduced to a modularoptical analytic system with fewer than 10 degrees of freedom acrosseach of its components, wherein the components are grouped intopre-configured modular subassemblies. These remaining degrees of freedommay be selected to optimize inter-component alignment tolerances whichwithout implementing active or frequent alignment processes. In someexamples, one or more control adjustments within one or more modularsubassemblies may be actuated using one or more corresponding actuatorsmounted in the subassemblies.

Sensors and/or detectors within one or more of the modular subassemblies(e.g., the CAM or the FTM) may be configured to transmit data to acomputer, the computer including a processor and non-transitory computerreadable media with machine-readable instructions stored thereon. Thesoftware may be configured to monitor optimal system performance, forexample, by detecting and analyzing beam focus, intensity, and shape. Insome implementations, the system may include an optical targetconfigured to display patterns specific to the alignment and performanceof each modular subassembly. The software may then indicate via agraphical user interface when a particular modular subassembly isoperating sub-optimally and recommend an open loop adjustment orimplement a course of closed loop action to rectify the issue. Forexample, the software may be configured to transmit signals to theactuators to reposition specific components within predeterminedtolerances, or may simply recommend swapping out the under-performingmodular sub-assembly. The software may be operated locally or remotelyvia a network interface, enabling remoted system diagnostics and tuning.

BRIEF DESCRIPTION OF THE DRAWINGS

The technology disclosed herein, in accordance with one or moreexamples, is described in detail with reference to the followingfigures. These figures are provided to facilitate the reader'sunderstanding of the disclosed technology, and are not intended to beexhaustive or to limit the disclosure to the precise forms disclosed.Indeed, the drawings in the figures are provided for purposes ofillustration only, and merely depict typical or example implementationsof the disclosed technology. Furthermore, it should be noted that forclarity and ease of illustration, the elements in the figures have notnecessarily been drawn to scale.

FIG. 1A illustrates a generalized block diagram of an example imagescanning system with which systems and methods disclosed herein may beimplemented.

FIG. 1B is a perspective view diagram illustrating an example modularoptical analytic system in accordance with examples disclosed herein.

FIG. 1C is a perspective view diagram illustrating an example precisionmounting plate in accordance with examples disclosed herein.

FIG. 1D illustrates a block diagram of an example modular opticalanalytic system consistent with examples disclosed herein.

FIG. 2A is a side view diagram illustrating an emission optical module(EOM) in accordance with examples disclosed herein.

FIG. 2B is a top-down diagram illustrating an EOM in accordance withexamples disclosed herein.

FIG. 3A is a back view diagram illustrating a focus tracking module(FTM) in accordance with examples disclosed herein.

FIG. 3B is a side view diagram illustrating an FTM in accordance withexamples disclosed herein.

FIG. 3C is a top-down view diagram illustrating an FTM in accordancewith examples disclosed herein.

FIG. 4A is a side view diagram illustrating an example modular opticalanalytic system in accordance with examples disclosed herein.

FIG. 4B is a block diagram illustrating an example configuration for atube lens subassembly from an EOM, in accordance with examples disclosedherein.

FIG. 4C is a block diagram illustrating another example configurationfor a tube lens subassembly from an EOM, in accordance with examplesdisclosed herein.

FIG. 5A is a side view diagram illustrating an FTM and an EOM withexamples disclosed herein.

FIG. 5B is a top-down view diagram illustrating an example FTM and anEOM in accordance with examples disclosed herein.

FIG. 6 is a side view diagram illustrating a line generation module(LGM) and an EOM in accordance with examples disclosed herein.

FIG. 7 is a top-down view diagram illustrating a LGM and an EOM inaccordance with examples disclosed herein.

FIG. 8 is a diagram illustrating an example process for installing andconfiguring a modular optical analytic system in accordance withexamples disclosed herein.

FIG. 9 illustrates an example computing engine that may be used inimplementing various features of examples of the disclosed technology.

It should be understood that the disclosed technology can be practicedwith modification and alteration, and that the disclosed technology belimited only by the claims and the equivalents thereof.

DETAILED DESCRIPTION

Some examples disclosed herein provide a modular optical system, such asones that may be used for analyzing biological samples. Other examplesdisclosed herein provide methods for assembling and installing modularoptical systems for analyzing biological samples. One such opticalsystem may be, or may be part of a genomic sequencing instrument. Theinstrument may be used to sequence DNA, RNA, or other biologicalsamples. Some genomic sequencing instruments operate by focusingcoherent or incoherent light sources operating at different wavelengthsthrough internal optics and onto the sample. Base pairs present in thesample then fluoresce and return light through the optics of thesequencer and onto an optical sensor, which can then detect the types ofbase pairs present. These types of instruments rely on precise alignmentand tuning of the internal optics and are sensitive to drifting ormisalignment of components caused by thermal effects (e.g., by heat fromthe light sources and electronics), as well as mechanical effects suchas vibrations or incidental contact from users. Examples of the presentdisclosure address these problems, and the installation and maintenancecosts associated therewith, through a modular approach. Groupings offunctionally related optical components may be pre-packaged, tested, andaligned as modular subassemblies. Each modular subassembly then may betreated as a field replaceable unit (FRU) which may be installed andaligned to the other modular subassemblies in the system by mounting thesubassembly to a precision alignment plate.

Some implementations provide a system including a plurality of modularsubassemblies and a precision mounting plate or, wherein each modularsubassembly includes an enclosure and a plurality of optical componentsaligned to the enclosure. The enclosure may include a plurality ofprecision mounting structures, and each modular subassembly may bemechanically coupled to the precision mounting plate, such that eachprecision mounting structure from a modular subassembly attachesdirectly to a corresponding precision mounting structure located on theprecision mounting plate or an adjacent modular subassembly. In someexamples, the line generation module includes a first light sourceoperating at a first wavelength, a second light source operating at asecond wavelength, and a beam shaping lens aligned at a predeterminedangle to each light source. For example, the first wavelength may be agreen or a blue wavelength and the second wavelength may be a red or agreen wavelength. The beam shaping lens may be a Powell lens.

In some implementations, the emissions optics module may include anobjective lens that is optically coupled to a light generation module,and a tube lens that is optically coupled to the objective lens. Theobjective lens focuses light onto a flow cell positioned at apredetermined distance from the flow cell. The objective may articulatealong a longitudinal axis, and the tube lens may include a lenscomponent that also articulates along a longitudinal axis within thetube lens to ensure accurate imaging. For example, the lens componentmay move to compensate for spherical aberration caused by articulationof the objective to image one or more surfaces of the flow cell.

In some examples, the flow cell may include a translucent cover plate, asubstrate, and a liquid sandwiched therebetween, and a biological samplemay be located at an inside surface of the translucent cover plate or aninside surface of the substrate. For example, the biological sample mayinclude DNA, RNA, or another genomic material which may be sequenced.

The focus tracking module may include a focus tracking light source anda focus tracking sensor, wherein the light source may generate a lightbeam, transmit the light beam through the plurality of opticalcomponents such that the light beam terminates at the focus trackingsensor. The focus tracking sensor may be communicatively coupled to aprocessor and a non-transitory computer readable medium withmachine-readable instructions stored thereon. The machine-readableinstructions, when executed, may cause the processor to receive anoutput signal from the focus tracking sensor and analyze the outputsignal to determine a set of characteristics of the light beam. In someimplementations, the machine-readable instructions, when executed,further cause the processor to generate a feedback signal indicatingthat one or more of the optical components should be reconfigured tooptimize the set of characteristics of the light beam. One or more ofthe modular subassemblies may be a field replaceable unit. The precisionmounting structures may include a slot, a datum, a tab, a pin, or arecessed cavity, other mechanical mounting structures as known in theart, or any combination thereof.

In some examples, the camera module includes a plurality of opticalsensors, and the light generation module includes a plurality of lightsources, wherein each optical sensor may be oriented to receive anddetect a light beam from corresponding light source.

Before describing various examples of the systems and methods disclosedherein, it is useful to describe an example environment with which thesystems and methods can be implemented. One such example environment isthat of an optical system, such as that illustrated in FIG. 1A. Theexample optical system may include a device for obtaining or producingan image of a region. The example outlined in FIG. 1 shows an exampleimaging configuration of a backlight design example.

As can be seen in the example of FIG. 1A, subject samples are located onsample container 110 (e.g., a flow cell as disclosed herein), which ispositioned on a sample stage 170 under an objective lens 142. Lightsource 160 and associated optics direct a beam of light, such as laserlight, to a chosen sample location on the sample container 110. Thesample fluoresces and the resultant light is collected by the objectivelens 142 and directed to a photo detector 140 to detect the florescence.Sample stage 170 is moved relative to objective lens 142 to position thenext sample location on sample container 110 at the focal point of theobjective lens 142. Movement of sample stage 110 relative to objectivelens 142 can be achieved by moving the sample stage itself, theobjective lens, the entire optical stage, or any combination of theforegoing. Further examples may also include moving the entire imagingsystem over a stationary sample.

Fluid delivery module or device 100 directs the flow of reagents (e.g.,fluorescent nucleotides, buffers, enzymes, cleavage reagents, etc.) to(and through) sample container 110 and waste valve 120. In particularexamples, the sample container 110 can be implemented as a flow cellthat includes clusters of nucleic acid sequences at a plurality ofsample locations on the sample container 110. The samples to besequenced may be attached to the substrate of the flow cell, along withother optional components.

The system also comprises temperature station actuator 130 andheater/cooler 135 that can optionally regulate the temperature ofconditions of the fluids within the sample container 110. Camera system140 can be included to monitor and track the sequencing of samplecontainer 110. Camera system 140 can be implemented, for example, as aCCD camera, which can interact with various filters within filterswitching assembly 145, objective lens 142, and focusing laser/focusinglaser assembly 150. Camera system 140 is not limited to a CCD camera andother cameras and image sensor technologies can be used.

Light source 160 (e.g., an excitation laser within an assemblyoptionally comprising multiple lasers) or other light source can beincluded to illuminate fluorescent sequencing reactions within thesamples via illumination through fiber optic interface 161 (which canoptionally comprise one or more re-imaging lenses, a fiber opticmounting, etc). Low watt lamp 165, focusing laser 150, and reversedichroic 185 are also presented in the example shown. In some examplesfocusing laser 150 may be turned off during imaging. In other examples,an alternative focus configuration can include a second focusing camera(not shown), which can be a quadrant detector, a Position SensitiveDetector (PSD), or similar detector to measure the location of thescattered beam reflected from the surface concurrent with datacollection.

Although illustrated as a backlit device, other examples may include alight from a laser or other light source that is directed through theobjective lens 142 onto the samples on sample container 110. Samplecontainer 110 can be ultimately mounted on a sample stage 170 to providemovement and alignment of the sample container 110 relative to theobjective lens 142. The sample stage can have one or more actuators toallow it to move in any of three dimensions. For example, in terms ofthe Cartesian coordinate system, actuators can be provided to allow thestage to move in the X, Y and Z directions relative to the objectivelens. This can allow one or more sample locations on sample container110 to be positioned in optical alignment with objective lens 142.

A focus (z-axis) component 175 is shown in this example as beingincluded to control positioning of the optical components relative tothe sample container 110 in the focus direction (typically referred toas the z axis, or z direction). Focus component 175 can include one ormore actuators physically coupled to the optical stage or the samplestage, or both, to move sample container 110 on sample stage 170relative to the optical components (e.g., the objective lens 142) toprovide proper focusing for the imaging operation. For example, theactuator may be physically coupled to the respective stage such as, forexample, by mechanical, magnetic, fluidic or other attachment or contactdirectly or indirectly to or with the stage. The one or more actuatorscan be configured to move the stage in the z-direction while maintainingthe sample stage in the same plane (e.g., maintaining a level orhorizontal attitude, perpendicular to the optical axis). The one or moreactuators can also be configured to tilt the stage. This can be done,for example, so that sample container 110 can be leveled dynamically toaccount for any slope in its surfaces.

Focusing of the system generally refers to aligning the focal plane ofthe objective lens with the sample to be imaged at the chosen samplelocation. However, focusing can also refer to adjustments to the systemto obtain a desired characteristic for a representation of the samplesuch as, for example, a desired level of sharpness or contrast for animage of a test sample. Because the usable depth of field of the focalplane of the objective lens may be small (sometimes on the order of 1 μmor less), focus component 175 closely follows the surface being imaged.Because the sample container is not perfectly flat as fixtured in theinstrument, focus component 175 may be set up to follow this profilewhile moving along in the scanning direction (herein referred to as they-axis).

The light emanating from a test sample at a sample location being imagedcan be directed to one or more detectors 140. Detectors can include, forexample a CCD camera. An aperture can be included and positioned toallow only light emanating from the focus area to pass to the detector.The aperture can be included to improve image quality by filtering outcomponents of the light that emanate from areas that are outside of thefocus area. Emission filters can be included in filter switchingassembly 145, which can be selected to record a determined emissionwavelength and to cut out any stray laser light.

In various examples, sample container 110 can include one or moresubstrates upon which the samples are provided. For example, in the caseof a system to analyze a large number of different nucleic acidsequences, sample container 110 can include one or more substrates onwhich nucleic acids to be sequenced are bound, attached or associated.In various examples, the substrate can include any inert substrate ormatrix to which nucleic acids can be attached, such as for example glasssurfaces, plastic surfaces, latex, dextran, polystyrene surfaces,polypropylene surfaces, polyacrylamide gels, gold surfaces, and siliconwafers. In some applications, the substrate is within a channel or otherarea at a plurality of locations formed in a matrix or array across thesample container 110.

Although not illustrated, a controller can be provided to control theoperation of the scanning system. The controller can be implemented tocontrol aspects of system operation such as, for example, focusing,stage movement, and imaging operations. In various examples, thecontroller can be implemented using hardware, algorithms (e.g., machineexecutable instructions), or a combination of the foregoing. Forexample, in some implementations the controller can include one or moreCPUs or processors with associated memory. As another example, thecontroller can comprise hardware or other circuitry to control theoperation, such as a computer processor and a non-transitory computerreadable medium with machine-readable instructions stored thereon. Forexample, this circuitry can include one or more of the following: fieldprogrammable gate array (FPGA), application specific integrated circuit(ASIC), programmable logic device (PLD), complex programmable logicdevice (CPLD), a programmable logic array (PLA), programmable arraylogic (PAL) or other similar processing device or circuitry. As yetanother example, the controller can comprise a combination of thiscircuitry with one or more processors.

Although the systems and methods may be described herein from time totime in the context of this example system, this is only one examplewith which these systems and methods may be implemented. After readingthis description, one of ordinary skill in the art will understand howthe systems and methods described herein can be implemented with thisand other scanners, microscopes and other imaging systems.

Examples of the technology disclosed herein provide modular opticalanalytic systems and methods. FIG. 1B is a perspective view diagramillustrating an example modular optical analytic system 180. System 180may include a plurality of modular subassemblies. For example, in someexamples, system 180 comprises four subassembly modules: line generationmodule (LGM) 182, focus tracking module (FTM) 184, camera module (CAM)186, and emission optical module (EOM) 188. As used herein in thecontext of the LGM, FTM, EOM, or CAM, a module refers to a hardware unit(e.g., a modular subassembly).

In some examples, LGM 182 may include one or more light sources. In someexamples, the one or more light sources may include coherent lightsources, such as laser diodes. In some examples, LGM 182 may include afirst light source configured to emit light in red or green wavelengths,and a second light source configured to emit light in green or bluewavelengths. LGM 182 may further include optical components, such asfocusing surfaces, lenses, reflective surfaces, or mirrors. The opticalcomponents may be positioned within an enclosure of LGM 182 as to directand focus the light emitted from the one or more light sources into anadjacent modular subassembly. One or more of the optical components ofLGM 182 may also be configured to shape the light emitted from the oneor more light sources into desired patterns. For example, in someexamples, the optical components may shape the light into line patterns(e.g., by using one or more Powel lenses, or other beam shaping lenses,diffractive or scattering components). One or more of the opticalcomponents may be located in one or more of the other modularsubassemblies. One or more of the modular subassemblies may also includeone or more field replaceable sub-components. For example, LGM 182 mayinclude one or more laser modules which may be individually removed fromLGM 182 and replaced.

In some examples, the adjacent modular subassembly (coupled to LGM 182)may be EOM 188. Light from the one or more light sources of LGM 182 maybe directed out of LGM 182 and into EOM 188 through an interface baffleattached to LGM 182 and/or EOM 188. For example, the interface bafflemay be an aperture shaped to enable light to pass through its center,while obscuring interference from external light sources. EOM 188 mayalso include an objective, a tube lens, and or other optical componentsconfigured to shape, direct, and/or focus fluorescent light excited bythe one or more light sources of LGM 182.

Light passing through EOM 188 may be directed into one of the otheradjacent modular subassemblies, for example, CAM 186, through aninterface port. CAM 188 may include one or more light sensors. In someexamples, a first light sensor may be configured to detect light fromthe first light source of LGM 182 (e.g., in a red or green wavelength),and a second light sensor may be configured to detect light from thesecond light source of LGM 182 (e.g., a green or blue wavelength). Thelight sensors of CAM 186 may be positioned within an enclosure in aconfiguration such as to detect light from two incident light beamswherein the incident light beams may be spaced apart by a predetermineddistance (e.g., between 1 mm and 10 mm) based on the pitch of the twosensors. In some implementations, the first light sensor and the secondlight sensor may be spaced apart from each other by between 3 mm and 8mm. The light sensors may have a detection surface sufficiently sized toallow for beam drift, for example, due to thermal effects or mechanicalcreep. Output data from the light sensors of CAM 186 may be communicatedto a computer processor. The computer processor may then implementcomputer software program instructions to analyze the data and report ordisplay the characteristics of the beam (e.g., focus, shape, intensity,power, brightness, position) to a graphical user interface (GUI), and/orautomatically control actuators and laser output to optimize the laserbeam. Beam shape and position may be optimized by actuating internaloptics of system 180 (e.g., tilting mirrors, articulating lenses, etc.).

FTM 184 may also couple to EOM 188 through an interface port. FTM 184may include instruments to detect and analyze the alignment and focus ofall of the optical components in system 180. For example, FTM 184 mayinclude a light source (e.g., a laser), optics, and a light sensor, suchas a digital camera or CMOS chip. The laser may be configured totransmit light source and optics may be configured to direct lightthrough optical components in system 180 and the light sensor may beconfigured to detect light being transmitted through optical componentsin system 180 and output data to a computer processor. The computerprocessor may then implement computer software program instructions toanalyze the data and report or display the characteristics of the laserbeam (e.g., focus, intensity, power, brightness, position) to agraphical user interface (GUI), and/or automatically control actuatorsand laser output to optimize the laser beam. In some examples, FTM 184may include a cooling system, such as an air or liquid cooling system asknown in the art.

In some examples, LGM 182 may include light sources that operate athigher powers to also accommodate for faster scanning speeds (e.g., thelasers in LGM 182 may operate at a five times greater power output).Similarly, the light source of laser module 184 may operate at a higheroutput power and/or may also include a high resolution optical sensor toachieve nanometer scale focus precision to accommodate for fasterscanning speeds. The cooling system of FTM 184 may be enhanced toaccommodate the additional heat output from the higher powered laserusing cooling techniques known in the art.

In one implementation, each modular subassembly may mechanically coupleto one or more other modular subassemblies, and/or to a precisionmounting plate 190. In some examples, precision mounting plate 190 maymechanically couple to a stage assembly 192. Stage assembly 192 mayinclude motion dampers, actuators to actuate one or more componentswithin one or more modular subassemblies, cooling systems, and/or otherelectronics or mechanical components as known in the art.

The modular subassemblies may be prefabricated, configured, andinternally aligned. In some implementations, a control unit may beelectronically coupled to stage assembly 192 and communicatively coupledto a user interface to enable automatic or remote manual alignment ofone or more modular subassemblies after they have been coupled toprecision mounting plate 190. Each modular subassembly may be a fieldreplaceable unit (FRU), such that it may be removed from precisionmounting plate 190 and replaced with another functionally equivalentmodular subassembly without disturbing the alignment or configuration ofthe other modular subassemblies in the system.

Each module is pre-aligned and pre-qualified before integration intosystem 180. For example, assembly and configuration of LGM 182 mayinclude the mechanical coupling of one or more lasers or laser diodesinto an enclosure, and installation of control electronics to operatethe lasers or laser diodes. The entire LGM 182 may then be mounted on atest bed and operated to align the laser diodes within the enclosure, aswell as any optics or other components. The LGM enclosure may includeexternal mounting structures, such as mounting pins, datum, notches,tabs, slots, ridges, or other protrusions or indentations configured toalign the LGM 182 to the test bed, as well as to precision mountingplate 190 when installed in system 180. Once LGM 182 is configured andtested, it may be either installed in a system 182, or packaged andstored or shipped as a field replaceable unit (FRU).

Other modular subassemblies, such as FTM 184, CAM 186, or EOM 188, maybe similarly assembled, configured, and tested prior to installation onsystem 180. Each modular subassembly may be assembled using mechanicalcoupling methods to limit mobility of internal components within thesubassembly as desired. For example, components may be locked in placewith fasteners or welds to stop mobility of once the component isaligned to the other components or the enclosure of the modularsubassembly. Some components, as desired, may be coupled witharticulating joints or allowed to move within an enclosure such thattheir relative orientation may be adjusted after installation onprecision mounting plate 190. For example, each modular subassembly'srelative positioning may be controlled precisely using predeterminedmechanical tolerances (e.g., by aligning datum to receiving notches inan adjoining modular subassembly or in precision mounting plate 190)such as to enable overall optical alignment of system 180 with a limitednumber of adjustable degrees of freedom (e.g., fewer than 10 overalldegrees of freedom in some examples).

FIG. 1C is a perspective view diagram illustrating an example precisionmounting plate 190. Precision mounting plate 190 may be fabricated fromlight weight, rigid, and heat tolerant materials. In someimplementations, precision mounting plate 190 may be fabricated from ametal (e.g., aluminum), ceramic, or other rigid materials as known inthe art. Precision mounting plate 190 may include precision alignmentstructures configured to mechanically couple to corresponding precisionalignment structures incorporated on the enclosures or housings of oneor more of the modular subassemblies. For example, precision alignmentstructures may include mounting pins, datums, tabs, slots, notches,grommets, magnets, ridges, indents, and/or other precision mountingstructures shaped to align a first surface (e.g., on precision mountingplate 190) to a second surface (e.g., an outer surface of the enclosureor housing of a modular subassembly. Referring to FIG. 1C, exampleprecision mounting plate 190 may include a plurality of LGM precisionmounting structures 194 configured to accept and mechanically couple tocorresponding precision mounting structures located on an outer surfaceof the enclosure of LGM 182. Similarly, precision mounting plate 190 mayinclude a plurality of EOM precision mounting structures 196 configuredto accept and mechanically couple to corresponding precision mountingstructures located on an outer surface of the enclosure of EOM 188. Bylocating LGM 182 and EOM 188 onto precision mounting plate 190 using theprecision mounting structures, LGM 182 and EOM 188 will align to eachother. Precision alignment structures located on the enclosures of othermodular subassemblies (e.g., FTM 184 and CAM 186) may then mechanicallycouple to respective precision alignment structures located on theenclosures of either LGM 182 or EOM 188, or on precision mounting plate190.

FIG. 1D illustrates a block diagram of an example modular opticalanalytic system. In some examples, a modular optical analytic system mayinclude an LGM 1182 with two light sources, 1650 and 1660, disposedtherein. Light sources 1650 and 1660 may be laser diodes which outputlaser beams at different wavelengths (e.g., red, green, or blue light).The light beams output from laser sources 1650 and 1660 may be directedthrough a beam shaping lens or lenses 1604. In some examples, a singlelight shaping lens may be used to shape the light beams output from bothlight sources. In other examples, a separate beam shaping lens may beused for each light beam. In some examples, the beam shaping lens is aPowell lens, such that the light beams are shaped into line patterns.

LGM 1182 may further include mirror 1002 and semi-reflective mirror 1004configured to direct the light beams through a single interface port toEOM 1188. The light beams may pass through a shutter element 1006. EOM1188 may include objective 1404 and a z-stage 1024 which moves objective1404 longitudinally closer to or further away from a target 1192. Forexample, target 1192 may include a liquid layer 1550 and a translucentcover plate 1504, and a biological sample may be located at an insidesurface of the translucent cover plate as well an inside surface of thesubstrate layer located below the liquid layer. The z-stage may thenmove the objective as to focus the light beams onto either insidesurface of the flow cell (e.g., focused on the biological sample). Thebiological sample may be DNA, RNA, proteins, or other biologicalmaterials responsive to optical sequencing as known in the art.

EOM 1188 may also include semi-reflective mirror 1020 to direct lightthrough objective 1404, while allowing light returned from target 1192to pass through. In some examples, EOM 1188 may include a tube lens 1406and a corrective lens 1450. Corrective lens 1450 may be articulatedlongitudinally either closer to or further away from objective 1404using a z-stage 1022 as to ensure accurate imaging, e.g., to correctspherical aberration caused by moving objective 1404. Light transmittedthrough corrective lens 1450 and tube lens 1406 may then pass throughfilter element 1012 and into CAM 1186. CAM 1186 may include one or moreoptical sensors 1050 to detect light emitted from the biological samplein response to the incident light beams.

In some examples, EOM 1188 may further include semi-reflective mirror1018 to reflect a focus tracking light beam emitted from FTM 1184 ontotarget 1192, and then to reflect light returned from target 1192 backinto FTM 1184. FTM 1184 may include a focus tracking optical sensor todetect characteristics of the returned focus tracking light beam andgenerate a feedback signal to optimize focus of objective 1404 on target1192.

FIGS. 2A and 2B are diagrams illustrating precision mounting structureson EOM 188. In several implementations, EOM 188 may include an EOMenclosure 210. EOM 188 may mechanically and optically couple to LGM 182,FTM 184, and CAM 186 (e.g., the enclosure of EOM 188 may include one ormore apertures corresponding to and aligned with an aperture located onan enclosure of each of the other modular subassemblies to enable light,generated by a light source(s) in LGM 182 and/or FTM 184 to transitthrough the apertures and internal optics of EOM 188). As illustrated inFIG. 2B, EOM enclosure 210 may include FTM precision mounting structures212 configured to align and mechanically couple (e.g., physicallyattach) to corresponding precision mounting structures located on anouter surface of an enclosure of FTM 184. Similarly, EOM enclosure 210may include CAM mounting structures 222 configured to align andmechanically couple to corresponding precision mounting structureslocated on an outer surface of an enclosure 220 of CAM 186.

FIGS. 3A, 3B, and 3C are diagrams illustrating precision mountingstructures on FTM 184. Referring to FIG. 3A, FTM 184 may include a lightsource and optical sensors positioned within FTM enclosure 300. FTMenclosure 300 may include interface ports for electronic interfaces 302,304, and 306 to control the light source and optical sensors. FTMenclosure 300 may also include precision mounting structures 312 (e.g.,precision mounting feet configured to mechanically couple to recesses orpredetermined locations on precision mounting plate 190). FTM enclosure300 may further include precision mounting structures 314 configured toalign and mechanically couple to corresponding precision mountingstructures 212 located on an outer surface of EOM enclosure 210

Pre-assembling, configuring, aligning, and testing each modularsubassembly, and then mounting each to precision mounting plate 190 toassist in system alignment, may reduce the amount of post-installationalignment required to meet desired tolerances. In one example, postinstallation alignment between EOM 188 and each of the other subassemblymodules may be accomplished by interfacing corresponding module ports(e.g., an EOM/FTM port, an EOM/CAM port, and an EOM/LGM port), andaligning the modular subassemblies to each other by manually orautomatically articulating the position (in the X, Y, or Z axis), angle(in the X or Y direction), and the rotation of each modular subassembly.Some of the degrees of freedom may be limited by precision alignmentstructures that predetermine the position and orientation of the modularsubassembly with respect to precision mounting plate 190 and adjacentmodular subassemblies. Tuning and aligning the internal optics of system180 may then be accomplished by articulating components internal to themodular subassemblies (e.g., by tilting or moving in either X, Y, or Zmirrors and lenses).

FIG. 4A is a side view diagram illustrating an example modular opticalanalytic system. As illustrated in FIG. 4A, LGM 182 and EOM 188 may bealigned and mechanically coupled to precision mounting plate 190, aswell as to each other. EOM 188 may include an objective 404 aligned, viamirror 408 with tube lens 406, which in turn is optically coupled to LGM182, such that light beams generated by LGM 182 transmit through aninterface baffle between LGM 182 and EOM 188, pass through objective404, and strike an optical target. Responsive light radiation from thetarget may then pass back through objective 404 and into tube lens 406.Tube lens 406 may include a lens element 450 configured to articulatealong the z-axis to correct for spherical aberration artifactsintroduced by objective 404 imaging through varied thickness of flowcell substrate or cover glass. For example, FIGS. 4B and 4C are blockdiagrams illustrating different configurations of tube lens 406. Asillustrated, lens element 450 may be articulated closer to or furtheraway from objective 404 to adjust the beam shape and path.

In some implementations, EOM 188 may be mechanically coupled to az-stage, e.g., controlled by actuators on alignment stage 192. In someexamples, the z-stage may be articulated by a precision coil andactuated by a focusing mechanism which may adjust and moves objective404 to maintain focus on a flow cell. For example, the signal to controlto adjust the focus may be output from FTM 184. This z-stage may alignthe EOM optics, for example, by articulating objective 404, tube lens406, and/or lens element 450.

FIGS. 5A and 5B are diagrams illustrating FTM 184. FTM 184 may interfacewith EOM 188 through FTM/EOM interface port 502. As illustrated in FIG.5A, light beams originating in FTM 184 and passing through the optics ofEOM 188 may reflect off flow cell 504. As disclosed herein, FTM 184 maybe configured to provide feedback to a computer processor in order tocontrol alignment and positioning of optical components throughoutsystem 180. For example, FTM 184 may employ a focus mechanism using twoor more parallel light beams which pass through objective 404 andreflect off flow cell 504. Movement of the flow cell away from anoptimal focus position may cause the reflected beams to change angle asthey exit objective 404. That angle may be measured by an optical sensorlocated in FTM 184. In some examples, the distance of the light pathbetween the optical sensor surface and the objective 404 may be between300 mm and 700 mm distance. FTM 184 may initiate a feedback loop usingan output signal from the optical sensor to maintain a pre-determinedlateral separation between beam spot patterns of the two or moreparallel light beams by adjusting the position of objective 404 usingthe z-stage in the EOM.

Some implementations of system 180 provide a compensation method for topand bottom surface imaging of flow cell 504. In some examples, flow cell504 may include a cover glass layered on a layer of liquid and asubstrate. For example, the cover glass may be between about 100 um andabout 500 um thick, the liquid layer may be between about 50 um andabout 150 um thick, and the substrate may be between about 0.5 and about1.5 mm thick. In one example, a DNA sample may be introduced at the topand bottom of the liquid channel (e.g., at the top of the substrate, andbottom of the cover glass). To analyze the sample, the focal point ofthe incident light beams at various depths of flow cell 504 may beadjusted by moving the z-stage (e.g., to focus on the top of thesubstrate or the bottom of the cover glass. Movement of objective 404 tochange incident beam focal points within flow cell 504 may introduceimaging artifacts or defects, such as spherical aberration. To correctfor these artifacts or defects, lens element 450 within tube lens 406may be moved closer to or further away from objective 404.

In some examples FTM 184 may be configured as a single FRU with noreplaceable internal components. To increase longevity and reliabilityof FTM internal components, such as the laser, laser output may bereduced (for example, below 5 mW).

FIGS. 6 and 7 are diagrams illustrating LGM 182 and EOM 188. Asillustrated, LGM 182 may interface with EOM 188 through LGM/EOMinterface baffle 602. LGM 182 is a photon source for system 180. One ormore light sources (e.g., light sources 650 and 660) may be positionedwithin an enclosure of LGM 182. Light generated from light sources 650and 660 may be directed through a beam shaping lens 604 and into theoptical path of EOM 188 through LGM/EOM interface baffle 602. Forexample, light source 650 may be a green laser and light source 660 maybe a red laser. In some implementations, light source 650 may be a bluelaser and light source 660 may be a green laser. The lasers may operateat high powers (e.g., more than 3 Watts). One or more beam shapinglenses 604 may be implemented to shape the light beams generated fromthe light sources into desired shapes (e.g., a line).

Photons generated by light sources 650 and 660 (e.g., green or bluewavelength photons and red or green wavelength photons) may excitefluorophores in DNA located on flow cell 504 to enable analysis of thebase pairs present within the DNA. High speed sequencing employs highvelocity scanning to deliver a sufficient photon dose to the DNAfluorophores, to stimulate sufficient emission of reactive photons fromthe DNA sample to be detected by the light sensors in CAM 186.

Beam shaping lens 604 may be a Powell lens that spreads the Gaussianlight emitted by lasers 650 and 660 into a uniform profile (inlongitudinal direction), which resembles a line. In someimplementations, a single beam shaping 604 lens may be used for multiplelight beams (e.g., both a red and a green light beam) which may beincident on the front of beam shaping lens 604 at differentpre-determined angles (e.g., plus or minus a fraction of a degree) togenerate a separate line of laser light for each incident laser beam.The lines of light may be separated by a pre-determined distance toenable clear detection of separate signals, corresponding to each lightbeam, by the multiple optical sensors in CAM 186. For example, a greenlight beam or a blue light beam may ultimately be incident on a firstoptical sensor in CAM 186 and a red light beam or a green light beam mayultimately be incident on a second optical sensor in CAM 186.

In some examples, the first and second light beams may becoincident/superimposed as they enter beam shaping lens 604 and thenbegin to fan out into respective line shapes as they reach objective404. The position of the beam shaping lens may be controlled with tighttolerance near or in close proximity to light sources 650 and 660 tocontrol beam divergence and optimize shaping of the light beams, i.e.,by providing sufficient beam shape (e.g., length of the line projectedby the light beam) while still enabling the entire beam shape to passthrough objective 404 without clipping any light. In some examples,distance between beam shaping lens 604 and objective 404 is less thanabout 150 mm.

In some implementations, system 180 may further comprise a modularsubassembly having a pocket to receive the optical target. The body maycomprise aluminum that includes a pigment having a reflectivity of nomore than about 6.0%. The body may include an inset region located atthe top surface and surrounding the pocket. The modular subassembly mayfurther comprise a transparent grating layer mounted in the inset regionand may be positioned above the optical target and spaced apart from theoptical target by a fringe gap. The body may include a pocket to receivethe optical target. The body may include a diffusion well located belowthe optical target. The diffusion well may receive excitation lightpassing through the optical target. The diffusion well may include awell bottom having a pigment based finish that exhibits a reflectivelyof no more than about 6.0%.

One of the modular subassemblies of system 180 may further include anoptical detection device. Objective 404 may emit excitation light towardthe optical target and receive fluorescence emission from the opticaltarget. An actuator may be configured to position objective 404 to aregion of interest proximate to the optical target. The processor maythen execute program instructions for detecting fluorescence emissionfrom the optical target in connection with at least one of opticalalignment and calibration of an instrument.

In some examples, objective 404 may direct excitation light onto theoptical target. The processor may derive reference information from thefluorescence emission. The processor may utilize the referenceinformation in connection with the at least one of optical alignment andcalibration of the instrument. The optical target may be permanentlymounted at a calibration location proximate to objective 404. Thecalibration location may be separate from flow cell 504. The solid bodymay represent a substrate comprising a solid host material with thefluorescing material embedded in the host material. The solid body mayrepresent at least one of an epoxy or polymer that encloses quantum dotsthat emit fluorescence in one or more predetermined emission bands ofinterest when irradiated by the excitation light.

FIG. 8 is a diagram illustrating an example process for installing andconfiguring a modular optical analytic system 800. Process 800 mayinclude positioning a plurality of light sources and a beam shaping lenswithin a first subassembly at step 805. For example, the plurality oflight sources may include light source 650 and light source 660. Thefirst subassembly may be an LGM, which may include an LGM enclosure towhich the light sources are mounted and aligned. The beam shaping lensmay be a Powell lens, also mounted within the LGM enclosure, andconfigured to shape light beams generated by light sources 650 and 660into separate line patterns.

Process 800 may also include positioning a tube lens and objectivewithin a second subassembly at step 815. For example, the secondsubassembly may be an EOM and may include an EOM enclosure to which theobjective and tube lens are mounted and aligned.

Process 800 may also include positioning a plurality of optical sensorswithin a third subassembly at step 825. For example, the thirdsubassembly may be a CAM and may include a CAM enclosure to which theoptical sensors are aligned and mounted. There may be a correspondingoptical sensor to each light source from step 805.

Process 800 may also include positioning a focus tracking light sourceand optical sensor within a fourth subassembly at step 835. For example,the fourth subassembly may be an FTM and may include an FTM enclosure towhich the focus tracking light source and optical sensor are mounted.

In some implementations, process 800 may further include individuallytesting each subassembly at step 845. For example, testing may includeprecisely tuning and/or aligning the internal components of eachsubassembly to the subassembly's enclosure. Each subassembly may then bemechanically coupled to a precision mounting plate at step 855. Forexample, the precision mounting plate may be precision mounting plate190. The entire system may then be aligned and tuned by powering thefocus tracking light source in the fourth subassembly and capturing anoutput signal from the focus tracking optical sensor of the fourthsubassembly to find an optimal focus of the optical target. The outputsignal from the target may be input into a computer processor configuredto analyze the characteristics of light beams generated by the focustracking light source, and then provide feedback to actuators on one ormore of the subassemblies, or to a graphical user interface to enabletuning of the optical components to optimize beam shape, power, andfocus.

As noted above, in various examples an actuator can be used to positionthe sample stage relative to the optical stage by repositioning eitherthe sample stage or the optical stage (or parts thereof), or both toachieve the desired focus setting. In some implementations,piezoelectric actuators can be used to move the desired stage. In otherexamples, a voice coil actuator can be used to move the desired stage.In some applications, the use of a voice coil actuator can providereduced focusing latency as compared to its piezoelectric counterparts.For examples using a voice coil actuator, coil size may be chosen as aminimum coil size needed to provide the desired movement such that theinductance in the coil can also be minimized. Limiting coil size, andtherefore limiting its inductance, provides quicker reaction times andrequires less voltage to drive the actuator.

As described above, regardless of the actuator used, focus informationfrom points other than a current sample location can be used todetermine the slope or the magnitude of change in the focus setting forscanning operations. This information can be used to determine whetherto feed the drive signal to the actuator earlier and how to set theparameters of the drive signal. Additionally, in some implementationsthe system can be pre-calibrated to allow drive thresholds to bedetermined for the actuator. For example, the system can be configuredto supply to the actuator drive signals at different levels of controloutput to determine the highest amount of control output (e.g., themaximum amount of drive current) the actuator can withstand withoutgoing unstable. This can allow the system to determine a maximum controloutput amount to be applied to the actuator.

As used herein, the term engine may describe a given unit offunctionality that can be performed in accordance with one or moreexamples of the technology disclosed herein. As used herein, an enginemay be implemented utilizing any form of hardware, software, or acombination thereof. For example, one or more processors, controllers,ASICs, PLAs, PALs, CPLDs, FPGAs, logical components, software routinesor other mechanisms may be implemented to make up an engine. Inimplementation, the various engines described herein may be implementedas discrete engines or the functions and features described can beshared in part or in total among one or more engines. In other words, aswould be apparent to one of ordinary skill in the art after reading thisdescription, the various features and functionality described herein maybe implemented in any given application and can be implemented in one ormore separate or shared engines in various combinations andpermutations. Even though various features or elements of functionalitymay be individually described or claimed as separate engines, one ofordinary skill in the art will understand that these features andfunctionality can be shared among one or more common software andhardware elements, and such description shall not require or imply thatseparate hardware or software components are used to implement suchfeatures or functionality.

Where components or engines of the technology are implemented in wholeor in part using software, in one example, these software elements canbe implemented to operate with a computing or processing engine capableof carrying out the functionality described with respect thereto. Onesuch example computing engine is shown in FIG. 9. Variousimplementations are described in terms of this example computing engine900. After reading this description, it will become apparent to a personskilled in the relevant art how to implement the technology using othercomputing engines or architectures.

Referring now to FIG. 9, computing engine 900 may represent, forexample, computing or processing capabilities found within desktop,laptop and notebook computers; hand-held computing devices (PDA's, smartphones, cell phones, palmtops, etc.); mainframes, supercomputers,workstations or servers; or any other type of special-purpose orgeneral-purpose computing devices as may be desirable or appropriate fora given application or environment. Computing engine 900 may alsorepresent computing capabilities embedded within or otherwise availableto a given device. For example, a computing engine may be found in otherelectronic devices such as, for example, digital cameras, navigationsystems, cellular telephones, portable computing devices, modems,routers, WAPs, terminals and other electronic devices that may includesome form of processing capability.

Computing engine 900 may include, for example, one or more processors,controllers, control engines, or other processing devices, such as aprocessor 904. Processor 904 may be implemented using a general-purposeor special-purpose processing engine such as, for example, amicroprocessor, controller, or other control logic. In the illustratedexample, processor 904 is connected to a bus 902, although anycommunication medium can be used to facilitate interaction with othercomponents of computing engine 900 or to communicate externally.

Computing engine 900 may also include one or more memory engines, simplyreferred to herein as main memory 908. For example, preferably randomaccess memory (RAM) or other dynamic memory, may be used for storinginformation and instructions to be executed by processor 904. Mainmemory 908 may also be used for storing temporary variables or otherintermediate information during execution of instructions to be executedby processor 904. Computing engine 900 may likewise include a read onlymemory (“ROM”) or other static storage device coupled to bus 902 forstoring static information and instructions for processor 904.

The computing engine 900 may also include one or more various forms ofinformation storage mechanism 910, which may include, for example, amedia drive 912 and a storage unit interface 920. The media drive 912may include a drive or other mechanism to support fixed or removablestorage media 914. For example, a hard disk drive, a floppy disk drive,a magnetic tape drive, an optical disk drive, a CD or DVD drive (R orRW), or other removable or fixed media drive may be provided.Accordingly, storage media 914 may include, for example, a hard disk, afloppy disk, magnetic tape, cartridge, optical disk, a CD or DVD, orother fixed or removable medium that is read by, written to or accessedby media drive 912. As these examples illustrate, the storage media 914can include a computer usable storage medium having stored thereincomputer software or data.

In alternative examples, information storage mechanism 910 may includeother similar instrumentalities for allowing computer programs or otherinstructions or data to be loaded into computing engine 900. Suchinstrumentalities may include, for example, a fixed or removable storageunit 922 and an interface 920. Examples of such storage units 922 andinterfaces 920 can include a program cartridge and cartridge interface,a removable memory (for example, a flash memory or other removablememory engine) and memory slot, a PCMCIA slot and card, and other fixedor removable storage units 922 and interfaces 920 that allow softwareand data to be transferred from the storage unit 922 to computing engine900.

Computing engine 900 may also include a communications interface 924.Communications interface 924 may be used to allow software and data tobe transferred between computing engine 900 and external devices.Examples of communications interface 924 may include a modem orsoftmodem, a network interface (such as an Ethernet, network interfacecard, WiMedia, IEEE 802.XX or other interface), a communications port(such as for example, a USB port, IR port, RS232 port Bluetooth®interface, or other port), or other communications interface. Softwareand data transferred via communications interface 924 may be carried onsignals, which can be electronic, electromagnetic (which includesoptical) or other signals capable of being exchanged by a givencommunications interface 924. These signals may be provided tocommunications interface 924 via a channel 928. This channel 928 maycarry signals and may be implemented using a wired or wirelesscommunication medium. Some examples of a channel may include a phoneline, a cellular link, an RF link, an optical link, a network interface,a local or wide area network, and other wired or wireless communicationschannels.

In this document, the terms “computer program medium” and “computerusable medium” are used to generally refer to media such as, forexample, memory 908, storage unit 920, media 914, and channel 928. Theseand other various forms of computer program media or computer usablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processing device for execution. Such instructionsembodied on the medium, are generally referred to as “computer programcode” or a “computer program product” (which may be grouped in the formof computer programs or other groupings). When executed, suchinstructions may enable the computing engine 900 to perform features orfunctions of the disclosed technology as discussed herein.

While various examples of the disclosed technology have been describedabove, it should be understood that they have been presented by way ofexample only, and not of limitation. Likewise, the various diagrams maydepict an example architectural or other configuration for the disclosedtechnology, which is done to aid in understanding the features andfunctionality that can be included in the disclosed technology. Thedisclosed technology is not restricted to the illustrated examplearchitectures or configurations, but the desired features can beimplemented using a variety of alternative architectures andconfigurations. Indeed, it will be apparent to one of skill in the arthow alternative functional, logical or physical partitioning andconfigurations can be implemented to implement the desired features ofthe technology disclosed herein. Also, a multitude of differentconstituent engine names other than those depicted herein can be appliedto the various partitions. Additionally, with regard to flow diagrams,operational descriptions and method claims, the order in which the stepsare presented herein shall not mandate that various examples beimplemented to perform the recited functionality in the same orderunless the context dictates otherwise.

It should be appreciated that all combinations of the foregoing concepts(provided such concepts are not mutually inconsistent) are contemplatedas being part of the inventive subject matter disclosed herein. Inparticular, all combinations of claimed subject matter appearing at theend of this disclosure are contemplated as being part of the inventivesubject matter disclosed herein. For example, although the disclosedtechnology is described above in terms of various examples andimplementations, it should be understood that the various features,aspects and functionality described in one or more of the individualexamples are not limited in their applicability to the particularexample with which they are described, but instead can be applied, aloneor in various combinations, to one or more of the other examples of thedisclosed technology, whether or not such examples are described andwhether or not such features are presented as being a part of adescribed example. Thus, the breadth and scope of the technologydisclosed herein should not be limited by any of the above-describedexamples.

Terms and phrases used in this document, and variations thereof, unlessotherwise expressly stated, should be construed as open ended as opposedto limiting. As examples of the foregoing: the term “including” shouldbe read as meaning “including, without limitation” or the like; the term“example” is used to provide example instances of the item indiscussion, not an exhaustive or limiting list thereof; the terms “a” or“an” should be read as meaning “at least one,” “one or more” or thelike; and adjectives such as “conventional,” “traditional,” “normal,”“standard,” “known” and terms of similar meaning should not be construedas limiting the item described to a given time period or to an itemavailable as of a given time, but instead should be read to encompassconventional, traditional, normal, or standard technologies that may beavailable or known now or at any time in the future. Likewise, wherethis document refers to technologies that would be apparent or known toone of ordinary skill in the art, such technologies encompass thoseapparent or known to the skilled artisan now or at any time in thefuture.

The term “coupled” refers to direct or indirect joining, connecting,fastening, contacting or linking, and may refer to various forms ofcoupling such as physical, optical, electrical, fluidic, mechanical,chemical, magnetic, electromagnetic, communicative or other coupling, ora combination of the foregoing. Where one form of coupling is specified,this does not imply that other forms of coupling are excluded. Forexample, one component physically coupled to another component mayreference physical attachment of or contact between the two components(directly or indirectly), but does not exclude other forms of couplingbetween the components such as, for example, a communications link(e.g., an RF or optical link) also communicatively coupling the twocomponents. Likewise, the various terms themselves are not intended tobe mutually exclusive. For example, a fluidic coupling, magneticcoupling or a mechanical coupling, among others, may be a form ofphysical coupling.

The presence of broadening words and phrases such as “one or more,” “atleast,” “but not limited to” or other like phrases in some instancesshall not be read to mean that the narrower case is intended or requiredin instances where such broadening phrases may be absent. The use of theterm “engine” does not imply that the components or functionalitydescribed or claimed as part of the engine are all configured in acommon package. Indeed, any or all of the various components of anengine, whether control logic or other components, can be combined in asingle package or separately maintained and can further be distributedin multiple groupings or packages or across multiple locations.

Additionally, the various examples set forth herein are described interms of exemplary block diagrams, flow charts and other illustrations.As will become apparent to one of ordinary skill in the art afterreading this document, the illustrated examples and their variousalternatives can be implemented without confinement to the illustratedexamples. For example, block diagrams and their accompanying descriptionshould not be construed as mandating a particular architecture orconfiguration.

We claim:
 1. A system comprising: a plurality of modular subassembliesand a plate; wherein each modular subassembly comprises an enclosure anda plurality of optical components aligned to the enclosure, and eachenclosure comprises a plurality of structures; and wherein each modularsubassembly is mechanically coupled to the plate by attachment of afirst structure of the modular subassembly directly to a correspondingsecond structure located on the plate, such that by mechanicallycoupling each modular subassembly to the plate using the first structureof the modular subassembly and the corresponding second structure on theplate, adjacent modular subassemblies are aligned to each other uponsuch attachment, and wherein two of the modular subassembliesmechanically coupled to the plate are also attached to each other bymechanically coupling an alignment structure on one of the two modularsubassemblies to a respective alignment structure on the other of thetwo modular subassemblies; wherein the plurality of modularsubassemblies comprises a first subassembly, wherein the firstsubassembly comprises a first light source operating at a firstwavelength and disposed within the first subassembly, and a second lightsource operating at a second wavelength and disposed within the firstsubassembly; wherein the plurality of modular subassemblies furthercomprises a second subassembly, wherein the second subassembly comprisesa focus tracking light source disposed within the second subassembly anda focus tracking sensor disposed within the second subassembly, whereinthe focus tracking light source is separate from the first and secondlight sources; and wherein the plurality of modular subassembliesfurther comprises a third subassembly, wherein the third subassemblycomprises: an objective lens and a tube lens optically coupled to theobjective lens, the objective lens to focus light onto a flow cellpositioned at a predetermined distance from the objective lens, and asemi-reflective mirror configured to reflect a focus tracking light beamemitted from the focus tracking light source onto the flow cell, andconfigured to reflect light returned from the flow cell onto the focustracking sensor.
 2. The system of claim 1, wherein the plurality ofmodular subassemblies further comprise a camera subassembly.
 3. Thesystem of claim 1, wherein the first subassembly comprises a beamshaping lens aligned at a predetermined angle to each of the first andsecond light sources.
 4. The system of claim 3, wherein the firstwavelength is a green wavelength or a blue wavelength, the secondwavelength is a green wavelength or a red wavelength, and the beamshaping lens is a Powell lens.
 5. The system of claim 1, wherein theobjective lens is to articulate along a longitudinal axis to move afocal point of the objective lens with respect to one or more surfacesof the flow cell.
 6. The system of claim 1, wherein the flow cellcomprises a translucent cover plate, a substrate, and a liquidsandwiched therebetween, and a biological sample is located at an insidesurface of the translucent cover plate or an inside surface of thesubstrate.
 7. The system of claim 6, wherein the biological samplecomprises a DNA sample or an RNA sample.
 8. The system of claim 1,wherein: the focus tracking light source is to generate a light beam,and transmit the light beam through at least the plurality of opticalcomponents of the second subassembly such that the light beam terminatesat the focus tracking sensor; and the focus tracking sensor iscommunicatively coupled to a processor and a non-transitory computerreadable medium with machine-readable instructions stored thereon, andthe machine-readable instructions, when executed by the processor, causethe processor to: receive an output signal from the focus trackingsensor, and analyze the output signal to determine a set ofcharacteristics of the light beam.
 9. The system of claim 8, wherein themachine-readable instructions, when executed by the processor, furthercause the processor to generate a feedback signal indicating that one ormore of the optical components of another of the plurality of modularsubassemblies should be reconfigured to optimize the set ofcharacteristics of the light beam.
 10. The system of claim 1, wherein atleast one of the modular subassemblies is a field replaceable unit. 11.The system of claim 1, wherein the plurality of structures comprises atleast one of a slot, a datum, a tab, a pin, or a recessed cavity. 12.The system of claim 2, wherein the camera subassembly comprises aplurality of optical sensors, wherein each optical sensor is oriented toreceive and detect a fluorescent light beam emitted from an opticaltarget triggered in response to a light beam emitted from one of thefirst or second light sources.
 13. The system of claim 1, wherein thethird subassembly is alignable relative to the plate and the first andsecond subassemblies.
 14. A method comprising: disposing a plurality oflight sources within a first enclosure; disposing a tubular lens and anobjective lens within a second enclosure, the objective lens configuredto focus light onto a flow cell positioned at a predetermined distancefrom the objective lens; disposing a plurality of optical sensors withina third enclosure; disposing a focus tracking light source and a focustracking optical sensor within a fourth enclosure, wherein the focustracking light source is separate from the plurality of light sources;disposing a semi-reflective mirror within the second enclosure, thesemi-reflective mirror configured to reflect a focus tracking light beamemitted from the focus tracking light source onto the flow cell, andconfigured to reflect light returned from the flow cell onto the focustracking sensor; attaching a respective mounting structure of each ofthe first enclosure, the second enclosure, the third enclosure, and thefourth enclosure to a corresponding mounting structure located on aplate such that adjacent enclosures of the first enclosure, the secondenclosure, the third enclosure, and the fourth enclosure are aligned toeach other upon such attachment; and attaching two selected enclosuresof the first enclosure, the second enclosure, the third enclosure, andthe fourth enclosure to each other by mechanically coupling an alignmentstructure on one of the two selected enclosures to a respectivealignment structure on the other of the two selected enclosures.
 15. Themethod of claim 14, further comprising disposing a beam shaping lenswithin the first enclosure.
 16. The method of claim 15, furthercomprising testing and aligning the plurality of light sources and thebeam shaping lens to the first enclosure before mounting the firstenclosure to the mounting plate.
 17. The method of claim 14, furthercomprising: generating a feedback signal using the focus trackingsensor; and reorienting the tube lens, the objective lens, or the secondenclosure, in response to the feedback signal.
 18. The method of claim17 further comprising articulating the objective lens along alongitudinal axis to move a focal point of the objective lens withrespect to one or more surfaces of the flow cell.
 19. The method ofclaim 17, further comprising fabricating the flow cell by sandwiching aliquid between a translucent cover plate and a substrate, and disposinga biological sample on the one or more surfaces of the flow cell. 20.The method of claim 19, further comprising locating the biologicalsample at a top surface and a bottom surface of the liquid, wherein thebiological sample comprises a DNA sample or an RNA sample.
 21. Themethod of claim 14, further comprising: aligning the second enclosurerelative to the plate and the first, third and fourth subassemblies.